Acyl-CoA dehydrogenases are a family of flavoproteins that catalyse the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with the concomitant reduction of enzyme-bound FAD. Different family members share a high sequence identity, catalytic mechanisms, and structural properties, but differ in the position of their catalytic bases and in their substrate binding specificity. Butyryl-CoA dehydrogenase prefers short chain substrates, medium chain- and long-chain acyl-CoA dehydrogenases prefer medium and long chain substrates, respectively, and Isovaleryl-CoA dehydrogenase prefers branched-chain substrates.The monomeric enzyme is folded into three domains of approximately equal size, where the N-terminal domain is all-alpha, the middle domain is an open barrel, and the C-terminal domain is a four-helical bundle. This entry represents the C-terminal domain found in medium chain acyl-CoA dehydrogenases, as well as in the related peroxisomal acyl-CoA oxidase-II enzymes, where this domain occurs as a tandem duplication. Acyl-CoA oxidase (ACO; ) catalyzes the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids.